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diff PaDEL/temp.dir/padelnew.xml.1 @ 0:68300206e90d draft default tip

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author deepakjadmin
date Thu, 05 Nov 2015 02:41:30 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PaDEL/temp.dir/padelnew.xml.1	Thu Nov 05 02:41:30 2015 -0500
@@ -0,0 +1,67 @@
+<tool id="PaDEL789xsf1" name="PaDEL">
+<description>"PaDEL Descriptor Calculation Tool"</description>
+<command interpreter="java -jar">PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $3d  $fingerprint $retainorder -file $output1 -log >$log  </command>
+
+<inputs>
+	<param format="txt" name="input" type="data" label="sdf file"/>
+  		
+	<param name="detectaromaticity" type="select" label="Detect the aroamaticity">
+        	<option value = "-detectaromaticity" selected="TRUE" >YES</option>
+		<option value = "" >NO</option>
+	</param>
+
+	<param name="removesalt" type="select" label="Remove salt">
+        	<option value = "-removesalt" selected="TRUE" >YES</option>
+		<option value = "" >NO</option>
+	</param>
+       
+        <param name="standardizenitro" type="select" label="Standardize nitro groups">
+        	<option value = "-standardizenitro" selected="TRUE" >YES</option>
+          	<option value = "" >NO</option>
+	</param>
+       
+        <param name="convert3d" type="select" label="convert in 3D">
+        	<option value = "" selected="TRUE" >NO</option>
+        	<option value = "-convert3d" >YES</option>
+  	</param>
+
+        <param name="retain3d" type="select" label="Retain 3D coordinates">
+        	<option value = "" selected="TRUE" >NO</option>
+        	<option value = "-retain3d" >YES</option>
+         	
+	</param>
+	
+	<param name="3d" type="select" label="calculate 3d descriptors">
+		<option value = "" selected="TRUE" >NO</option>
+		<option value = "-3d" >YES</option>
+	</param>
+
+	<param name="fingerprint" type="select"  label="calculate fingerprints">
+        	<option value = "" selected="TRUE" >NO</option>
+        	<option value = "-fingerprints">YES</option>
+	</param>
+
+	
+	<param name="retainorder" type="select" label="Retain molecules order">
+        	<option value = "-retainorder" selected="TRUE">YES</option>
+         	<option value = "" >NO</option>
+	</param>
+
+	
+	
+                  <!--
+<param name="3d" type="checkbox" label="Include 3D descriptors" description="add 3D descriptor" value="1" default="0" />
+<param name="fingerprint" type="checkbox" label="Include PubChem fingerprints" description="calculate 881 fingerprints" value="1" default="0" />
+-->
+	</inputs>
+
+<outputs>
+	<data format="txt" name="output1" label="Descriptors File"/>
+	<data format="txt" name="log" label="Log File"/>
+</outputs>
+
+<help>
+run command with sdf file format only and output file will be in CSV format.
+</help>
+
+</tool>